Infighting in recent weeks between jihadists and other rebels in northern Syria that led to the assassination of two Free Syrian Army commanders is likely to worsen, compounding a power struggle within rebel ranks at a time when an emboldened Syrian President Bashar al-Assad is gaining major battlefield advances with the backing of Lebanese Hezbollah fighters and is threatening to retake the crucial city of Homs.
In order to confront the FSA with a common jihadist front, al-Qaeda affiliates Jabhat al-Nusra and the Islamic State of Iraq and Syria (ISIS) appear to be shelving their own highly public disagreement over leadership authority. “They have managed their dispute,” says former Libyan jihadist Norman Benotman. “Their disagreement is still there but I think because of pressure from other jihadists and key al-Qaeda figures they have reached a way of working together and the jihadist forums are now playing down any divisions.” 
ISIS was formed officially in April when the leader of al-Qaeda’s Iraq branch, Abu Bakr al-Baghdadi, announced that his group would be merging with Jabhat al-Nusra. The new combined group, he said, would expand its activities across the area of the eastern Mediterranean (AP, April 10; June 15). His announcement prompted an open dispute with al-Nusra leader Abu Muhammad al-Golani, who, along with some other fighters, refused to operate under the ISIS banner.
In what appears to be a strategy designed to encourage both jihadist groups to come under the greater sway of core al-Qaeda, the Pakistani Taliban has dispatched scores of fighters and is establishing camps in northern Syria (Reuters, July 14). According to Taliban commanders in Pakistan, the men were sent because: “our Arab brothers have come here for our support, we are bound to help them in their respective countries and that is what we did in Syria” (Reuters, July 14). The presence of the Taliban will likely help the top al-Qaeda leadership resolve lingering differences and mediate future quarrels between their two affiliated groups in Syria, said a senior Lebanese intelligence officer. 
The Taliban are not the only foreign jihadists arriving in a new surge reinforcing al-Qaeda affiliates in Syria to fight Assad or strengthen the jihadists in any future confrontations with FSA-loyal rebels or Syrian Kurds. According to Jordanian jihadist leader Muhammad Shalabi (a.k.a. Abu Sayyaf), more than 700 experienced Jordanian fighters have been sent to Syria in recent months (al-Hayat, July 14).
Abu Sayyaf blames the FSA for the infighting that led to the July 11 slaying by ISIS militants of Kamal Hamami (a.k.a. Abu Basir), a member of the FSA’s Supreme Military Council. Hamami’s shooting was carried out in front of other members of the FSA’s Supreme Military Council and according to FSA sources the trigger was pulled by Abu Ayman al-Baghdadi, the Islamic State’s Amir of Syria’s coastal region. The flagrancy of the shooting suggests ISIS leaders feel they can act with impunity or have confidence they are strong enough to confound any retaliation.  A few days earlier, other ISIS militants beheaded Fadi al-Qish, a rebel commander in the northern province of Idlib. In the case of al-Qish his severed head—along with the head of one of his men—was left on the ground as a crude warning to others not to cross the jihadists.
The motives for Hamami’s shooting remain murky as it is still unclear whether it was a preplanned revenge for an operational disagreement or a killing prompted by Hamami’s refusal to lift a checkpoint blocking his killer’s path. Abu Sayyaf argues it was the former, saying that the FSA started the fighting (al-Hayat, July 14). That is not the viewpoint of FSA commanders, who are demanding Hamami’s killer be handed over to face trial before a Shari’a court in Aleppo. Insisting that “We do not instigate battles with anyone,” FSA spokesman Louay Almokdad says that the FSA has still not been informed as to why Hamami was killed, although he and other FSA commanders harbor suspicions that it was premeditated and sparked by differences over anti-Assad military operations in the area. 
Preplanned or not, Abu Sayyaf offers a clear line in on why jihadists and the FSA have clashed and why the intra-rebel violence is bound to increase: “There is a big difference between secular and Islamist fighters in terms of vision and purpose. For instance, the FSA wants a democratic secular regime to be imposed, and it does not have any problem with linking its positions to Western dictates once the regime falls.” The jihadists “want to implement the law of God, which will lead to an inevitable clash… we arrived in Syria to rule by God Almighty’s law. Many of those affiliated with the FSA were with the regime, and many have refused so far to cleanse themselves of the filth of Ba’athist rule; they declare that [the Ba’ath party] is secular. There are battalions in the FSA that ardently refuse to apply the Islamist system of government” (al-Hayat, July 14).
This latest bout of jihadist violence targeting the FSA comes after months of sharp rivalry between mainly foreign jihadists and more secular or religiously moderate Syrian-born rebels. It also foreshadowed the clashes in July that risk the development of a civil war within a civil war—a situation that will only strengthen Assad’s hand and further complicate the delivery of U.S. or Western arms to the uprising.
Since the killing of al-Waqqas the al-Qaeda influence on the Syrian rebellion has grown and not just on the battlefield, where the jihadists have demonstrated better fighting skills and greater expertise in strategy and coordination. Both the smaller al-Nusra and the larger ISIS have sought to exert more power when it comes to the local governance of rebel enclaves in northern Syria. This seems to have aggravated already tense relations between local FSA fighters and jihadists as they jostle for control over the civilian population and compete for grain stocks, flour production facilities and other government property, including oil wells that can generate significant revenue.
Nearly 400,000 barrels of crude oil were produced by wells around the city of Raqqa and in the desert region to the east before the civil war and the jihadists have been quick to seize control of them. The oil is typically sold to local entrepreneurs for refining in home-built mini-refineries that produce usable albeit poor quality petrol and kerosene for cooking and heating stoves. General Salim Idriss, the head of the FSA’s Supreme Military Council, has bristled at the jihadist control of the oil wells and recently asked for help from Western powers to seize the oilfields—an appeal likely to go unheeded (Daily Telegraph, May 18). The FSA, heavily divided, lacking funds and short on weapons, does not have the power to try to grab the oilfields itself, allowing the jihadists to continue to benefit economically and politically from the oil revenue.
The two jihadist groups have a different style when it comes to local governance, one of the root causes of the dispute between them. Al-Nusra has been less harsh in the city of Aleppo and some outlying towns than ISIS has been in the northeastern province of Raqqa, where locals complain of floggings and public executions of those jihadists deemed to be in breach of Islam.
In Aleppo and some northern villages, al-Nusra has limited its jihadi messages when interacting with locals in rebel-held territory and has talked more in terms of assisting the poor. In Aleppo, German filmmaker Marcel Mettelsiefen, who spent several weeks in the city, says: “You see streets being cleaned by al-Nusra and schools organized by al-Nusra… radical Islamists are doing well; they are very efficient and have more funds.” 
However, much of the al-Nusra work that attracted the praise of civilians – social outreach and distribution of war spoils and the contrast between the discipline of its fighters and the corruption of many in the FSA ranks (notorious for plundering and selling humanitarian aid for profit) is now being overshadowed by the less nuanced and far harsher ISIS interaction with locals. The conduct of ISIS in Syria is a reflection of the style of its commander, al-Baghdadi, a highly competent, if brutal, leader who is immersed in the tactics pursued by al-Qaeda in Iraq, where suicide bombings, the targeting of collaborators and beheadings of hostages have been standard tactics.
The ISIS regime has prompted a backlash, with occasional civilian protests in Raqqa and Deir al-Zor. According to a senior U.N. official, jihadists have also been interfering with the distribution of humanitarian aid. They have “gotten much more strident in diverting our convoys in the Deir al-Zor area where we have actually had commodities taken,” says the executive director of the World Food Program, Ertharin Cousin. “We cannot afford to have any political group—whichever side they are on—impacting humanitarian assistance and politicizing it.” 
Some FSA commanders say they will retaliate for the recent jihadist killings of their comrades. They say they have little alternative as the jihadists have been boasting they will kill more members of the FSA’s Supreme Military Council. While FSA leaderas command many more fighters, the jihadists are often better equipped and benefit from funding and supplies provided by wealthy ideological sympathizers in the Gulf and from the revenue they can generate from the oilfields. External support, overall discipline and the battlefield supremacy gained by the skills al-Qaeda learned in post-invasion Iraq have given the jihadists the edge in their struggle to take the leading role in the rebellion against the Assad regime.
Jamie Dettmer is an expert on North Africa, the Middle East and Southern Europe. He writes for Newsweek/Daily Beast, Voice of America and Maclean’s. He is also a Senior Media Fellow at the Democracy Institute.
1. Author’s phone interview with Noman Benotman, July 11, 2013.
2. Author’s interview with a senior Lebanese intelligence officer who requested anonymity, Beirut, Lebanon, July 17 2013.
3. Author’s phone and Skype interviews with several FSA commanders who requested anonymity, July 12, 13 and 14, 2013.
5. Author’s phone interview with Marcel Mettelsiefien, April 1, 2013.
6. Author’s interview with the executive director of the World Food Program, Ertharin Cousin, Beirut, Lebanon, June 26, 2013.